publicações selecionadas
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artigo académico
- The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber 2023
- IEC7871 Quercus suber model: The first multi-tissue diel cycle genome-scale metabolic model of a woody tree. BioRxiv. 2021
- Stringent response of Escherichia coli: revisiting the bibliome using literature mining. Microbial Informatics and Experimentation. 2011
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artigo de conferência
- Drug Target Identification based on the construction of a Genome-scale metabolic model for the human pathogen Candida parapsilosis 2022
- A computational approach to finding new drug targets for pathogenic Candida species 2021
- Identification of robust strain designs via tandem pFBA/LMOMA phenotype prediction 2017
- Towards the identification of pathways for lipids biosynthesis in HCB 2017
- Análise de fluxos metabólicos com substrato isotopicamente marcado (13C-MFA) em S. typhimurium 2016
- A computation tool for the estimation of biomass composition from genomic and transcriptomic information. AI Communications. 2016
- Development of an integrated framework for minimal cut set enumeration in constraint-based models. AI Communications. 2016
- Metabolic profiling of secreted fermentative byproducts by Salmonella typhimurium 2014
- Prediction of protein subunits using KEGG BRITE 2014
- Reconstructing genome-scale metabolic models with merlin : the Ashbya gossypii case study 2012
- Revealing new biotechnological potentialities of the riboflavin producer fungus Ashbya gossypii by means of the construction and analysis of its metabolic network 2011
- Towards genome-wide semi-automated transporter system annotations 2011
- Merlin: Metabolic models reconstruction using genome-scale information. IFAC proceedings volumes. 2010
- Adsorption equilibrium of fructose, glucose and sucrose for cationic resins in the sodium and potassium form 2009
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artigo de revista
- A Genome-Scale Metabolic Model for the Human Pathogen Candida Parapsilosis and Early Identification of Putative Novel Antifungal Drug Targets. Genes. 2022
- Inclusion of maintenance energy improves the intracellular flux predictions of CHO. PLoS Computational Biology. 2021
- Enhancing acetic acid and 5-hydroxymethyl furfural tolerance of C. saccharoperbutylacetonicum through adaptive laboratory evolution. Enzyme and Microbial Technology. 2021
- A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation. Biochemical SocIETy Transactions. 2020
- Genome-Scale Metabolic Model of the Human Pathogen Candida albicans: A Promising Platform for Drug Target Prediction. Journal of Fungi. 2020
- Metabolic engineering strategies for butanol production in Escherichia coli. Biotechnology and Bioengineering. 2020
- Discovery and implementation of a novel pathway for n-butanol production via 2-oxoglutarate. Biotechnology for Biofuels. 2019
- SamPler - a novel method for selecting parameters for gene functional annotation routines. BMC Bioinformatics. 2019
- iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6. Antibiotics. 2019
- Comparison of pathway analysis and constraint-based methods for cell factory design. BMC Bioinformatics. 2019
- Mapping Salmonella typhimurium pathways using 13C metabolic flux analysis. Metabolic Engineering. 2019
- An adsorptive bioprocess for production and recovery of resveratrol with Corynebacterium glutamicum. Journal of Chemical Technology and Biotechnology. 2018
- Impact of the cultivation strategy on resveratrol production from glucose in engineered Corynebacterium glutamicum. Antibiotics. 2018
- Methods for automated genome-scale metabolic model reconstruction. Biochemical SocIETy Transactions. 2018
- Genome-scale modeling of yeast: chronology, applications and critical perspectives. FEMS Yeast Research. 2017
- Development of a Framework for Metabolic Pathway Analysis-Driven Strain Optimization Methods. Interdisciplinary Sciences-Computational Life Sciences. 2017
- Genome-Wide Semi-Automated Annotation of Transporter Systems. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2017
- Integration of biomass formulations of genome-scale metabolic models with experimental data reveals universally essential cofactors in prokaryotes. Metabolic Engineering. 2017
- Improving the flux distributions simulated with genome-scale metabolic models of Saccharomyces cerevisiae. Metabolic Engineering Communications. 2016
- Estimation of biomass composition from genomic and transcriptomic information. Journal of Integrative Bioinformatics. 2016
- A Comparative Proteome Analysis of Escherichia coli ¿relA Mutant Cells. Frontiers in Bioengineering and Biotechnology. 2016
- Current state and challenges for dynamic metabolic modeling. Current Opinion in Microbiology. 2016
- Stoichiometric representation of geneproteinreaction associations leverages constraint-based analysis from reaction to gene-level phenotype prediction. PLoS Computational Biology. 2016
- Yeast metabolic chassis designs for diverse biotechnological products. Acta Cytologica. 2016
- A comparative analysis of dynamic models of the central carbon metabolism of Escherichia coli. IFAC-PapersOnLine. 2016
- Computing and applying atomic regulons to understand gene expression and regulation. Antibiotics. 2016
- Reconstructing genome-scale metabolic models with merlin. Nucleic Acids Research. 2015
- iOD907, the first genome-scale metabolic model for the milk yeast Kluyveromyces lactis. Antibiotics. 2014
- Dietary sugars analysis: quantification of fructooligossacharides during fermentation by HPLC-RI method. Frontiers in Nutrition. 2014
- Identification of Metabolic Engineering Targets through Analysis of Optimal and Sub-Optimal Routes. Antibiotics. 2013
- Metabolic responses to recombinant bioprocesses in Escherichia coli. Antibiotics. 2013
- Exploring the gap between dynamic and constraint-based models of metabolism. Metabolic Engineering. 2012
- Genome-wide metabolic (re-) annotation of Kluyveromyces lactis. BMC Genomics. 2012
- Influence of the RelA Activity on E. coli Metabolism by Metabolite Profiling of Glucose-Limited Chemostat Cultures. Metabolites. 2012
- State and specific growth estimation in heterologous protein production by Pichia pastoris. AIChE Journal. 2012
- A study of the short and long-term regulation of E. coli metabolic pathways. Journal of Integrative Bioinformatics. 2011
- Identification of minimal metabolic pathway models consistent with phenotypic data. Journal of Process Control. 2011
- Metabolic footprint analysis of recombinant Escherichia coli strains during fed-batch fermentations. Molecular Biosystems. 2011
- Modeling formalisms in Systems Biology. Amb Express. 2011
- Semantic annotation of biological concepts interplaying microbial cellular responses. BMC Bioinformatics. 2011
- Comparison of adsorption equilibrium of fructose, glucose and sucrose on potassium gel-type and macroporous sodium ion-exchange resins. Analytica Chimica Acta. 2010
- Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis–Menten and approximate kinetic equations. Biosystems. 2010
- OptFlux: An open-source software platform for in silico metabolic engineering. BMC Systems Biology. 2010
- Assessment of physiological conditions in E. coli fermentations by epifluorescent microscopy and image analysis . Biotechnology Progress. 2009
- @Note: A workbench for Biomedical Text Mining. Journal of Biomedical Informatics. 2009
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capítulo de livro
- Analyzing and designing cell factories with OptFlux. Methods in Molecular Biology. 2018
- Reconstructing High-Quality Large-Scale Metabolic Models with merlin. Methods in Molecular Biology. 2018
- Systems biology in fungi 2015
- Systems Biology in Fungi 2013
- A Systematic Modeling Approach to Elucidate the Triggering of the Stringent Response in Recombinant E. coli Systems 2011
- Interpreting the Regulatory Interplay in E. coli Metabolic Pathways 2011
- A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems. Computational Methods in Applied Sciences. 2009
- A Software Tool for the Simulation and Optimization of Dynamic Metabolic Models. Computational Methods in Applied Sciences. 2009
- Data Integration Issues in the Reconstruction of the Genome-Scale Metabolic Model of Zymomonas Mobillis 2009
- Evolutionary Approaches for Strain Optimization Using Dynamic Models under a Metabolic Engineering Perspective. Computational Methods in Applied Sciences. 2009
- Large Scale Dynamic Model Reconstruction for the Central Carbon Metabolism of Escherichia coli. Computational Methods in Applied Sciences. 2009
- Modelling of Biotechnological Processes – An Approach Based on Artificial Neural Networks. Studies in Computational Intelligence. 2009
- Evaluating Evolutionary Algorithms and Differential Evolution for the Online Optimization of Fermentation Processes. Computational Methods in Applied Sciences. 2007
- Evaluating Simulated Annealing Algorithms in the Optimization of Bacterial Strains. Computational Methods in Applied Sciences. 2007
- Evolutionary Algorithms for Static and Dynamic Optimization of Fed-batch Fermentation Processes 2005
- Evolutionary Algorithms for Optimal Control in Fed-Batch Fermentation Processes. Computational Methods in Applied Sciences. 2004
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documento
- Drug Target Identification based on the construction of a Genome-scale metabolic model for the human pathogen Candida parapsilosis 2022
- A computational approach to finding new drug targets for pathogenic Candida species 2021
- Molecular determinants of the SARS-CoV-2 fusion peptide activity 2021
- A reconciled version of the cork oak tree genome-scale metabolic model 2020
- Development of an integrated metabolic and transcriptional regulatory model for Saccharomyces cerevisiae 2020
- Towards metabolic optimization of CHO cells: in silico improvement of culture medium 2019
- Inferring optimal minimal medium on genome-scale metabolic models using evolutionary algorithms 2019
- Automated pathway curation and improving metabolic model reconstruction based on phylogenetic analysis of pathway conservation 2017
- Towards the identification of pathways for lipids biosynthesis in HCB 2017
- OptimModels: a framework for strain optimization using kinetic models 2017
- MIYeastK: The Metabolic Integrated Yeast Knowledgebase 2016
- Unveiling the molecular determinants responsible for NAD(P)(H) cofactor specificity using enzyme structural information 2016
- Developing novel pathways for butanol production in E. coli 2016
- Rational modular design of yeast strains towards overproduction of industrially relevant products 2016
- Development of pathway analysis based algorithms for strain optimization 2016
- Metabolic systems biology: tools for model-based analysis and design of microbial systems 2016
- New approaches for improving strain design methodologies 2015
- MEtabolic models Reconstruction using genome scaLe INformation (merlin) - assessment and validation 2015
- Merlin Latest Developments for Pathways Analysis 2015
- Towards a Genome-Scale Metabolic Model of the Streptococcus Pneumoniae R6 Avirulent Strain 2015
- Metabolic profiling of secreted fermentative byproducts by Salmonella typhimurium 2014
- Reconstruction of a genome-scale metabolic model for the filamentous fungus Ashbya gossypii 2014
- Reconstruction of a genome-scale metabolic model for the filamentous fungus Ashbya gossypii 2013
- Towards a genome-scale metabolic model for the Kluyveromyces lactis yeast. 2013
- Reconstructing genome-scale metabolic models with merlin : the Ashbya gossypii case study 2012
- Reconstruction of a genome-scale metabolic model for the filamentous fungus Ashbya gossypii 2012
- Reconstruction of a genome-scale metabolic model for the riboflavin producer fungus Ashbya gossypii 2012
- Metabolic reconstruction of less characterized microorganisms: a new methodology for reaction identification from genome sequencing data. 2009
- Specific growth rate regulation in a fed-batch E. coli fermentation 2007
- V Seminário de Investigação em Educação Matemática – Actas 1995